Pseudomonas population genomics: Difference between revisions

Revision as of 20:53, 18 June 2013

Build a local genome database
1. Database schema:
  1. "genome": genome_id, strain_name, ncbi_taxid
  2. "orf": genome_id, locus_tag, start, stop, strand, genome_name, product_name
  3. "orth_orf": orth_orf_id, locus_name, genome_id, orth_class
2. Parsing scripts
  1. Rayees Parsing code, requires that you remove columns 9-27 using bash command: cut -c 1-8 (I will write a bash script that does this and runs the program) https://www.dropbox.com/s/lpxxbkxeyw7frrn/parser.pl
3. Database loading scripts
Molecular Evolution of flagellum genes
1. Download orthologs
2. Reconstruct phylogenetic tree
3. Run PAML tests

Material and Methods
1. Protein ortholog data: fleN, fleQ, flhF
2. Protocol:
  1. Fasta headers are too long for tree, run: rename.pl to shorten names usage: >rename.pl FASTA file > OUTPUTfilename.fas editing/rule (script name?); Alignment (tool and command); Phylogeny; Tree display (R commands)

Gene	Alignment	Notes
fleN	fleN pep alignment	Conserved Domain
fleQ	fleQ pep alignment	Conserved Domain
flhf	flhF pep alignment	Conserved Domain

Finish parsing the genome files to upload the "orf" table (Raymond & Rayees)
1. Rayees Parsed genome files: https://www.dropbox.com/sh/k0zktvvmv39op9i/1zBercEky8
Parsing the ortholog file to upload the "orth_orf" table (Raymond)
Identify and download fleN, fleQ, and flhF orthologs & align them (Rayees)

@@ Line 17: / Line 17: @@
 ## Protein ortholog data: [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105676&start=1583956&stop=1584798&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleN], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=104960&start=1187587&stop=1189059&replicon_id_reference=136&alphabet=protein&limit_to_species=false fleQ], [http://pseudomonas.com/alignPolymorphicGeneSequencesStep1.do?feature_id_parent=105674&start=1582528&stop=1583817&replicon_id_reference=136&alphabet=protein&limit_to_species=false flhF]
 ## Protocol:
-### Fasta headers are too long for tree, run: [[File:renamer.pl]] editing/rule (script name?); Alignment (tool and command); Phylogeny; Tree display (R commands)
+### Fasta headers are too long for tree, run: [https://www.dropbox.com/s/x2p4joeqg7omfub/rename.pl rename.pl] to shorten names <code> usage: >rename.pl FASTA file > OUTPUTfilename.fas</code> editing/rule (script name?); Alignment (tool and command); Phylogeny; Tree display (R commands)
 {| class="wikitable"
 ! Gene !! Alignment !! Tree !! Notes